
PhD PROJECT DESCRIPTION: MarrowPatch: an injectable hematopoietic cell –
delivery system to study ectopic hematopoiesis for supportive care in hematology
From wooden leg prostheses to gold dental implants, humanity has long sought to restore lost limb, organ, or tissue function using biomaterials. With recent advances in regenerative medicine and the growing number of biomaterials entering clinical trials, new challenges and questions have emerged. Among them: rather than merely restoring lost function, could we engineer a gain of function? To explore this new direction, researchers are now developing ectopic biomaterial-based niches with engineered microenvironments designed to mimic the structure and function of native organs or tissues. These engineered systems open new avenues for deepening our fundamental understanding and hold the potential to enhance or even surpass natural biological functions.
In line with recent advancements in regenerative medicine and novel understanding of naturally occurring ectopic hematopoietic niches [Ref. 1] the Laboratory of Regenerative Haematopoiesis has developed an ectopic bone marrow artificial niche (eBMAN) system to decipher the role of the bone marrow (BM) microenvironment in hematopoiesis while also serving as an in situ blood cell factory [Ref. 2]. This advanced cell therapy combines BM stromal cells and hematopoietic stem and progenitor cells (HSPCs), seeded into a porous biomaterial and implanted in a minimally invasive fashion in the subcutaneous space. However, the ectopic nature of the host tissue presents several bottlenecks, including an adequate immune response to the biomaterial, promoting the de novo formation of a functional vascular network, and ensuring the survival an controlled expansion of transplanted cells for clinically meaningful periods of time. Ultimately, eBMAN has the potential to revolutionize tradituonal transfusion medicine and radically change outcomes for patients with BM dysfunction leading to severe cytopenia.
We are seeking funding for this position through the very competitive University of Lausanne Faculty of Biology and Medicine PhD 2026 fellowship program (application instructions here from August 22nd 2026). Other grant applications are ongoing for funding decisions in 2026-2027 and open positions will be posted in our lab website. Independently, inquiries from self-funded individuals interested in this project should be sent together with a CV, a motivation letter and at least one reference letter to both Prof. Naveiras (olaia.naveiras@unil.ch) and Dr. Bonini (fabien.bonini@unil.ch) with subject title “MarrowPatch position”.
As BM physiology meets biomaterial engineering, this project requires a deep understanding of biology and either a background in chemistry and physics to overcome these limitations, or a medical physiopathology background to complement the expertise of direct supervisor Dr. Fabien Bonini. The ideal candidate is an independent, flexible, reliable, enthusiastic, positive and collaborative-minded team player with strong interest in stem cell biology and animal work (Module 1/LTK certificate is advantageous but not mandatory). Experience in complex 2D or 3D culture systems, co-culture models or organoid technologies is highly desirable, as well as knowledge of flow cytometry and microscopy. Additional knowledge in biomaterials synthesis, chemistry (e.g., protein coupling), biomechanics, or haematology will be considered a plus.
[1] Schyrr F, Alonso-Calleja A, Vijaykumar A, Sordet-Dessimoz J, Gebhard S, Sarkis R, Bataclan C, Ferreira Lopes S, Oggier A, de Leval L, Nombela-Arrieta C, Naveiras O. Inducible CXCL12/CXCR4-dependent extramedullary hematopoietic niches in the adrenal gland. Blood. 2024
[2] Tavakol DN, Tratwal J, Bonini F*, Genta M, Campos V, Burch P, Hoehnel S, Béduer A, Alessandrini M, Naveiras O§, Braschler T§. Injectable, scalable 3D tissue-engineered model of marrow hematopoiesis. Biomaterials. 2020
MASTER’S THESIS POSITION:
Separation of primary cell adipocytes by Deterministic Lateral Displacement
This master thesis project focuses on the development of a novel Deterministic Lateral Displacement (DLD) platform tailored for sorting primary adipocytes obtained from human tissue biopsies. While DLD systems have demonstrated great potential in sorting various blood cell types, their application to isolating primary cells from tissue digestion remains largely unexplored. The goal of this project is to build upon a DLD device previously developed in our laboratory and expand its utility toward the efficient isolation of bone marrow adipocytes.
The thesis will involve redesigning and optimizing the existing DLD platform to accommodate the unique characteristics of primary adipocyte samples. Key objectives include adjusting the critical sorting size, modifying microfluidic geometries to manage heterogeneous cell populations, and implementing strategies to prevent chip clogging. A significant part of the project will also focus on optimizing the biological pre-processing of the tissue biopsy. This includes refining the digestion protocol to preserve fragile adipocytes, removing lipid contamination, and achieving a monophasic cell suspension suitable for microfluidic sorting. The student will work closely with both the Laboratory of Life Sciences Electronics (CLSE-EPFL) and the Laboratory of Regenerative Hematopoiesis (Naveiras group-UNIL) to iteratively test and improve both the biological and engineering aspects of the workflow.
Type of work: 10% literature study, 20% design and microfabrication, 25% cell culture and biological characterization, 25% microfluidic device testing, 20% data treatment and results reporting
Duration: 6 months
Prerequisites: Ideally, someone with a background in bioengineering, biology or chemistry, but physics or microtechnology are also welcome. A strong motivation is required regardless of your background.
Interested candidates are encouraged to contact us via email and include their CV. While a reference letter is not required, it would be considered an asset: micaela.cristofori@epfl.ch, fabien.bonini@unil.ch